Check Engine light caused by Cylinder 1 mis-firing

So I got a check engine warning on my boat. I took her to the dealer and they read the code off of the ECM. It was reporting that cylinder number one had miss-fired. The dealer attempted to flash the ECM on the boat, but the computer was telling them not to. They stopped and called Indmar who told them to ignore the warning and flash the ECM anyway.

Has anyone else had this issue? Is this a common problem on these boats?

By the way, the dealer told me that a check engine warning is common on these boats that is caused by the batteries falling below 10 volts. Apparently if you don't turn the battery switch off and pop the 50 amp breaker fuse the boat will continue to drain the batteries. When you hit 10 volts it causes a check engine warning light that has to be reset by the dealer after the batteries are charged.... seems like a way for dealer ships to make money! The ECM re-flashing cost me $120!